DNase-HS pipeline paired-end - Version 2

Status
released
Title
DNase-HS pipeline paired-end - Version 2
Assays
DNase-seq, genetic modification followed by DNase-seq
Description
ENCODE Uniform Processing Pipeline of DNase-seq Hypersensitive Sites for paired-end reads (DCC version 2). This pipeline inputs gzipped DNA-sequencing reads in the form of fastqs and a genome index. These fastqs come from technical replicates that are processed with bwa to generate unfiltered and filtered alignments (bam format). The filtered alignments, combined with a DNase mappability reference. More information could be found on the attached document or https://www.encodeproject.org/dnase-seq/.
Lab
ENCODE Processing Pipeline
Pipeline standards
DNase-seq Data Standards

Pipeline schematic